The reapers have returned from dark space. With Earth under attack and the mass relays in a state of chaos from refugees and the councils fleet engaging reaper forces the galaxy is a mess. The outcome is unknown, the warfare is devastating. The galaxy will never be the same.

Well, I think that the shipyard for frigates (and cruisers, if these also hve their own shipyard) will be Geth, as Geth ships will be forming the basic ships of Reapers. And Reapers will have capital shipyard, which will most likely have the tubes for the human paste :)

Or another option is, that Reapers will have two sets of shipyards, one for Geth, the other for Reapers. And the Collector cruiser... I dont know.

that reminds me, are you going to give the reaper shipyards Geth Architecture or are you going to give them a more Citadel esq style one because im almost certain thats where they make new reapers each cycle, aside from places like the collector base.